-----------------------
Start of variable list:
-----------------------
Sample_ID:
D3-MAA100040-3_11_M-1-1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/SRR
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Oct 12 19:44:32 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791074
Current job name : Step_02_D3-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791074.1.linga

Loading required modules...


List files in scratch directory:

total 72M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 D3-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  35M Oct 12 19:44 SRR6575176_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  38M Oct 12 19:44 SRR6575176_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575176_1.fastq <==
@SRR6575176.1 1/1
TTGATGCTGCGACCATGGATCACAATGGGACCATGCTGTTCTTTAAAGGGGAGTTTGTGTGGAGGGGTCACTCAGGGACCCGGGAGTTGATCTCAGCGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575176.2 2/1
GACCCTAGTGTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575176.3 3/1
CATTTACACCTACTACCCAACTATCCATAAATCTAAGTATAGCCATTCCACTATGAGCTGGAGCCGTAATTACAGGCTTCCGACACAAACTAAAAAGCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF
@SRR6575176.4 4/1
ACCAGGGTGCTCAGGTTGGCCGAGGTGCTGAACAACCCGGGGGGCAGGCTGCGGAGAGCATTGCGGGTCAGATCCAGGGCGCGCAGCCGGGGCACGGGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575176.5 5/1
TGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575176_2.fastq <==
@SRR6575176.1 1/2
NAGCATCCACTGAGGTGATGGGATTCTTCCACCTCGCTGAGATCAACTCCCGGGTCCCTGAGTGACCCCTCCACACAAACTCCCCTTTAAAGAACAGCAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575176.2 2/2
GTCTTAGGTATAGTAAATGTATTGAATCCATCATACGTCACAGAATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCGGAGCACTCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575176.3 3/2
ATACTAGAGTAGCTCCTCCGATTAGGTGTATTAATAAGTGTCCTGCAGTAATGTTAGCTGTAAGCCGGACTGCTAATGCCATTGGTTGAATAAATAGGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFF
@SRR6575176.4 4/2
GGGTAGCACCGTCTCCTGCCATGGTCCCACCGAGTTTCCGAGCTCCCTCCCTGCCGACACTGTCCATCTGTCGGTGGAATTCTCCAACCTGACGCAGCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575176.5 5/2
ATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTATGATGGATTCAATACATTTACTATACCTAAGACAGACTATGATAACTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF

Starting FASTQC command


Processing SRR6575176_1.fastq

Printing command:
fastqc --outdir SRR6575176_1.fastq

Analysis complete for SRR6575176_1.fastq

Processing SRR6575176_2.fastq

Printing command:
fastqc --outdir SRR6575176_2.fastq

Analysis complete for SRR6575176_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 407M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 D3-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 203M Oct 12 19:44 SRR6575176_1.fastq
-rw-r--r--    1 kkarri waxmanlab 203M Oct 12 19:44 SRR6575176_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:14 EDT 2018
0 hours, 0 minutes and 42 seconds elapsed.
==========================================================